1jcy

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[[Image:1jcy.gif|left|200px]]<br /><applet load="1jcy" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1jcy, resolution 1.90&Aring;" />
 
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'''Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium'''<br />
 
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==Overview==
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==Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium==
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We have determined the crystal structures of the metalloenzyme 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase from Aquifex aeolicus in complex with phosphoenolpyruvate (PEP) and ribose 5-phosphate (R5P), and with a bisubstrate inhibitor that mimics the postulated linear reaction intermediate. R5P, which is not a substrate for KDO8P synthase, binds in a manner similar to that of arabinose 5-phosphate (A5P), which is the natural substrate. The lack of reactivity of R5P appears to be primarily a consequence of the loss of a water molecule coordinated to Cd(2+) and located on the si side of PEP. This water molecule is no longer present because it cannot form a hydrogen bond with C2-OH(R5P), which is oriented in a different direction from C2-OH(A5P). The bisubstrate inhibitor binds with its phosphate and phosphonate moieties occupying the positions of the phosphate groups of A5P and PEP, respectively. One of the inhibitor hydroxyls replaces water as a ligand of Cd(2+). The current work supports a mechanism for the synthesis of KDO8P, in which a hydroxide ion on the si side of PEP attacks C2(PEP), forming a tetrahedral-like intermediate with a buildup of negative charge at C3(PEP). The ensuing condensation of C3(PEP) with C1(A5P) would be favored by a proton transfer from the phosphate moiety of PEP to the aldehyde carbonyl of A5P to generate the hydroxyl. Overall, the process can be described as a syn addition of water and A5P to the si side of PEP.
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<StructureSection load='1jcy' size='340' side='right'caption='[[1jcy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1jcy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JCY FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jcy OCA], [https://pdbe.org/1jcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jcy RCSB], [https://www.ebi.ac.uk/pdbsum/1jcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jcy ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/KDSA_AQUAE KDSA_AQUAE]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jcy_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jcy ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1JCY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with <scene name='pdbligand=R5P:'>R5P</scene>, <scene name='pdbligand=CD:'>CD</scene>, <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=PEP:'>PEP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCY OCA].
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*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
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__TOC__
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==Reference==
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</StructureSection>
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Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis., Wang J, Duewel HS, Woodard RW, Gatti DL, Biochemistry. 2001 Dec 25;40(51):15676-83. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11747443 11747443]
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[[Category: 3-deoxy-8-phosphooctulonate synthase]]
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[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Duewel, H S.]]
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[[Category: Duewel HS]]
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[[Category: Gatti, D L.]]
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[[Category: Gatti DL]]
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[[Category: Wang, J.]]
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[[Category: Wang J]]
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[[Category: Woodard, R W.]]
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[[Category: Woodard RW]]
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[[Category: CD]]
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[[Category: PEP]]
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[[Category: PO4]]
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[[Category: R5P]]
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[[Category: beta/alpha barrel]]
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[[Category: kdo]]
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[[Category: kdo8p]]
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[[Category: kdo8ps]]
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[[Category: pep]]
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[[Category: r5p]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:21:13 2008''
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Current revision

Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium

PDB ID 1jcy

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